Update r-archr to 1.0.3 #52121
Update r-archr to 1.0.3 #52121
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Caution Review failedThe pull request is closed. 📝 Walkthrough📝 WalkthroughThe pull request involves updates to the Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/r-archr/meta.yaml (1)
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1-103: Scope of changes exceeds typical version bumpWhile this PR is marked as a version bump, it includes several significant changes:
- Version update from 1.0.2 to 1.0.3
- License change from GPL-2.0-or-later to MIT
- Removal of r-base version constraint
- Addition of 6 new dependencies
These changes, particularly the license change and dependency modifications, warrant careful review and testing.
Consider:
- Testing the package with different r-base versions
- Documenting the rationale for the license change
- Verifying that all new dependencies are properly versioned
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📒 Files selected for processing (2)
recipes/r-archr/meta.yaml(8 hunks)recipes/r-archr/patches/0001-cap-threads.patch(0 hunks)
💤 Files with no reviewable changes (1)
- recipes/r-archr/patches/0001-cap-threads.patch
🧰 Additional context used
🪛 yamllint
recipes/r-archr/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/r-archr/meta.yaml (3)
1-1: Verify version and checksum authenticity
The version has been updated to 1.0.3 with a new SHA256 checksum.
#!/bin/bash
# Description: Verify version and checksum
# 1. Check latest release version
gh api repos/GreenleafLab/ArchR/releases/latest --jq .tag_name
# 2. Download and verify checksum
TEMP_DIR=$(mktemp -d)
cd $TEMP_DIR
curl -L https://github.com/GreenleafLab/ArchR/archive/refs/tags/v1.0.3.tar.gz -o source.tar.gz
echo "9c07c785a095062a998ed94c65df17a58f273d0d64062c14210f0a2c491304cf source.tar.gz" | sha256sum -c -Also applies to: 11-11
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
99-99: Verify license change and file existence
The license has been changed from GPL-2.0-or-later to MIT. This is a significant change that requires verification.
#!/bin/bash
# Description: Verify license change in upstream repository
# 1. Check license in DESCRIPTION file of the latest release
curl -sL https://github.com/GreenleafLab/ArchR/archive/refs/tags/v1.0.3.tar.gz | \
tar xz --to-stdout "*/DESCRIPTION" | \
rg "^License:"
# 2. Check if MIT license file exists in R share directory
ls -l $PREFIX/lib/R/share/licenses/MIT 2>/dev/null || echo "MIT license file not found"Also applies to: 101-101, 103-103
27-27: Consider maintaining r-base version constraint
The version constraint for r-base has been removed. This could potentially lead to compatibility issues with different R versions.
#!/bin/bash
# Description: Check r-base version constraints in similar packages
# Look for patterns of r-base version constraints in other recipes
fd -e yaml -e yml . recipes/ --exec rg -l 'r-base.*[0-9]'
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The license is a mess. I was confused why I had it as GPL back in my original PR #36855. Looks like the file |
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FYI, I'm going to temp make the test passing optional so I can get an artifact to locally debug. Please no merges until I revert that. 🙏 |
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@BiocondaBot please fetch artifacts |
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Package(s) built are ready for inspection:
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This fails in local tests as well. I've reported it at GreenleafLab/ArchR#2234 Looks like fragile assumptions about internal object structures. Probably need upper bound(s) on some (plotting?) dependencies. Not sure I'll get back to this before Monday. Additional eyes welcome! |
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Looks like the biocontainer build section does not properly find the testthat files that are loaded through the Log Snippet (link) 12:41:03 BIOCONDA INFO (ERR) [Nov 19 12:41:03] SERR Error: `path` does not exist
12:41:03 BIOCONDA INFO (ERR) [Nov 19 12:41:03] SERR Execution halted
12:41:03 BIOCONDA INFO (ERR) [Nov 19 12:41:03] ERRO Task processing failed: Unexpected exit code [1] of container [fe3a4865cc0f step-cf14308070], container preserved
12:41:03 BIOCONDA INFO (OUT) ...
12:41:03 BIOCONDA ERROR COMMAND FAILED (exited with 1): mulled-build build-and-test r-archr=1.0.3--r43hdbdd923_0 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && Rscript -e "library('"'"'ArchR'"'"')" && Rscript -e "testthat::test_file('"'"'tests/testthat.R'"'"', stop_on_failure=TRUE)"' --channels conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda --involucro-path /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/involucro
12:41:03 BIOCONDA ERROR TEST FAILED: recipes/r-archr |
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In the meantime, I can work around this by simply installing the tests with the package. Then they can be referenced implicitly. |
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Seems that the container also cannot handle |
this depends that `test.requires` are not installed for the container and checks lack of macs2 to skip
Update
r-archr: 1.0.2 → 1.0.3recipes/r-archr(click to view/edit other files)@GreenleafLabThis pull request was automatically generated (see docs).